[2023-06-05 02:12:13,774] [INFO] DFAST_QC pipeline started.
[2023-06-05 02:12:13,779] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 02:12:13,779] [INFO] DQC Reference Directory: /var/lib/cwl/stga34ad651-d18a-4630-8989-dc2b08ca400d/dqc_reference
[2023-06-05 02:12:15,601] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 02:12:15,602] [INFO] Task started: Prodigal
[2023-06-05 02:12:15,602] [INFO] Running command: gunzip -c /var/lib/cwl/stgcfff36f8-63a8-4f20-9c2e-a0a838a1dc6f/GCA_934162145.1_ERR7747426_bin.416_genomic.fna.gz | prodigal -d GCA_934162145.1_ERR7747426_bin.416_genomic.fna/cds.fna -a GCA_934162145.1_ERR7747426_bin.416_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 02:12:17,034] [INFO] Task succeeded: Prodigal
[2023-06-05 02:12:17,035] [INFO] Task started: HMMsearch
[2023-06-05 02:12:17,035] [INFO] Running command: hmmsearch --tblout GCA_934162145.1_ERR7747426_bin.416_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga34ad651-d18a-4630-8989-dc2b08ca400d/dqc_reference/reference_markers.hmm GCA_934162145.1_ERR7747426_bin.416_genomic.fna/protein.faa > /dev/null
[2023-06-05 02:12:17,257] [INFO] Task succeeded: HMMsearch
[2023-06-05 02:12:17,259] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgcfff36f8-63a8-4f20-9c2e-a0a838a1dc6f/GCA_934162145.1_ERR7747426_bin.416_genomic.fna.gz]
[2023-06-05 02:12:17,276] [INFO] Query marker FASTA was written to GCA_934162145.1_ERR7747426_bin.416_genomic.fna/markers.fasta
[2023-06-05 02:12:17,276] [INFO] Task started: Blastn
[2023-06-05 02:12:17,276] [INFO] Running command: blastn -query GCA_934162145.1_ERR7747426_bin.416_genomic.fna/markers.fasta -db /var/lib/cwl/stga34ad651-d18a-4630-8989-dc2b08ca400d/dqc_reference/reference_markers.fasta -out GCA_934162145.1_ERR7747426_bin.416_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:12:19,032] [INFO] Task succeeded: Blastn
[2023-06-05 02:12:19,036] [INFO] Selected 27 target genomes.
[2023-06-05 02:12:19,037] [INFO] Target genome list was writen to GCA_934162145.1_ERR7747426_bin.416_genomic.fna/target_genomes.txt
[2023-06-05 02:12:19,076] [INFO] Task started: fastANI
[2023-06-05 02:12:19,077] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfff36f8-63a8-4f20-9c2e-a0a838a1dc6f/GCA_934162145.1_ERR7747426_bin.416_genomic.fna.gz --refList GCA_934162145.1_ERR7747426_bin.416_genomic.fna/target_genomes.txt --output GCA_934162145.1_ERR7747426_bin.416_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 02:12:31,203] [INFO] Task succeeded: fastANI
[2023-06-05 02:12:31,204] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga34ad651-d18a-4630-8989-dc2b08ca400d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 02:12:31,204] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga34ad651-d18a-4630-8989-dc2b08ca400d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 02:12:31,207] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 02:12:31,207] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 02:12:31,207] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-06-05 02:12:31,209] [INFO] DFAST Taxonomy check result was written to GCA_934162145.1_ERR7747426_bin.416_genomic.fna/tc_result.tsv
[2023-06-05 02:12:31,210] [INFO] ===== Taxonomy check completed =====
[2023-06-05 02:12:31,210] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 02:12:31,211] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga34ad651-d18a-4630-8989-dc2b08ca400d/dqc_reference/checkm_data
[2023-06-05 02:12:31,214] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 02:12:31,228] [INFO] Task started: CheckM
[2023-06-05 02:12:31,228] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934162145.1_ERR7747426_bin.416_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934162145.1_ERR7747426_bin.416_genomic.fna/checkm_input GCA_934162145.1_ERR7747426_bin.416_genomic.fna/checkm_result
[2023-06-05 02:12:44,285] [INFO] Task succeeded: CheckM
[2023-06-05 02:12:44,287] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 02:12:44,306] [INFO] ===== Completeness check finished =====
[2023-06-05 02:12:44,307] [INFO] ===== Start GTDB Search =====
[2023-06-05 02:12:44,307] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934162145.1_ERR7747426_bin.416_genomic.fna/markers.fasta)
[2023-06-05 02:12:44,308] [INFO] Task started: Blastn
[2023-06-05 02:12:44,308] [INFO] Running command: blastn -query GCA_934162145.1_ERR7747426_bin.416_genomic.fna/markers.fasta -db /var/lib/cwl/stga34ad651-d18a-4630-8989-dc2b08ca400d/dqc_reference/reference_markers_gtdb.fasta -out GCA_934162145.1_ERR7747426_bin.416_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:12:45,122] [INFO] Task succeeded: Blastn
[2023-06-05 02:12:45,127] [INFO] Selected 26 target genomes.
[2023-06-05 02:12:45,127] [INFO] Target genome list was writen to GCA_934162145.1_ERR7747426_bin.416_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 02:12:45,136] [INFO] Task started: fastANI
[2023-06-05 02:12:45,137] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfff36f8-63a8-4f20-9c2e-a0a838a1dc6f/GCA_934162145.1_ERR7747426_bin.416_genomic.fna.gz --refList GCA_934162145.1_ERR7747426_bin.416_genomic.fna/target_genomes_gtdb.txt --output GCA_934162145.1_ERR7747426_bin.416_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 02:12:50,065] [INFO] Task succeeded: fastANI
[2023-06-05 02:12:50,077] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 02:12:50,078] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_902766875.1	s__RUG11215 sp902766875	78.6192	95	334	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG11215	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001916775.1	s__CAG-302 sp001916775	76.7837	56	334	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-302	95.0	95.82	95.12	0.84	0.77	8	-
GCA_900548425.1	s__CAG-302 sp900548425	76.7828	57	334	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-302	95.0	99.47	98.99	0.91	0.87	3	-
GCA_017432825.1	s__RUG11198 sp017432825	76.7154	58	334	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG11198	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905211265.1	s__HGM10818 sp905211265	76.4729	56	334	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__HGM10818	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 02:12:50,080] [INFO] GTDB search result was written to GCA_934162145.1_ERR7747426_bin.416_genomic.fna/result_gtdb.tsv
[2023-06-05 02:12:50,081] [INFO] ===== GTDB Search completed =====
[2023-06-05 02:12:50,085] [INFO] DFAST_QC result json was written to GCA_934162145.1_ERR7747426_bin.416_genomic.fna/dqc_result.json
[2023-06-05 02:12:50,085] [INFO] DFAST_QC completed!
[2023-06-05 02:12:50,085] [INFO] Total running time: 0h0m36s